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iCount is a Python module and associated command-line interface (CLI), which provides all the
commands needed to process protein-RNA iCLIP interaction data and to identify and quantify
sites of protein-RNA interactions on RNA.

iCount’s main input are FASTQ files with iCLIP sequencing data, its main output are BED files
with identified and quantified cross-linked sites.

A number of analyses are included in iCount that provide insights into the properties of
protein-RNA interaction.